Savage worlds then? I played in some really satisfying Deadlands games a while ago, with all the supernatural fluff stripped out and then added back in slowly. Sort of like we were discovering it all in what we thought was going to be a standard spaghetti western.

I can't help but go back to DFRPG if just for the magic system. Ditch the organizations and all rules associated with them. Get your players to help you develop fluff to fill in the power vacuums. I think if you tell them up front that this is a game built on the DFRPG rules, but without any of the story, you'll be fine. That's how Ttory_Seller's "The Last Escape" was billed, and despite half of us being Dresdenophiles, we're all having a great time.

I know this isn't FATE, but perhaps you could use the most recent Mutants and Masterminds book (4th? 3rd?) if you don't mind a little modification here and there.

As the game is based around superheroes/villains there has to be a ton of flexibility, and where the game really shines is in the super power creation sections. Everything has point-values with X amount for this strength of telekinesis or this large a fireball or what have you, which means that instead of having characters build powers as part of character gen, you simply allocate a certain number of points to make up spells with per turn/day/whatever increment you so choose.